PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40251-40300 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1836 | 98.6234 | 99.7502 | 77.6187 | 6018 | 84 | 5989 | 15 | 7 | 46.6667 | |
| gduggal-snapfb | INDEL | I1_5 | * | hetalt | 80.2098 | 77.5793 | 83.0249 | 77.6167 | 8685 | 2510 | 4128 | 844 | 445 | 52.7251 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 84.7522 | 77.5610 | 93.4132 | 77.6139 | 159 | 46 | 156 | 11 | 11 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 84.7522 | 77.5610 | 93.4132 | 77.6139 | 159 | 46 | 156 | 11 | 11 | 100.0000 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m0_e0 | homalt | 97.6237 | 95.7364 | 99.5868 | 77.6133 | 247 | 11 | 241 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | SNP | * | map_l125_m1_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 77.6119 | 30 | 0 | 30 | 0 | 0 | ||
| hfeng-pmm1 | SNP | tv | map_l125_m1_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 77.6119 | 30 | 0 | 30 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 34.8632 | 22.3938 | 78.6667 | 77.6119 | 58 | 201 | 59 | 16 | 16 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e0 | * | 99.3133 | 99.4247 | 99.2021 | 77.6100 | 20394 | 118 | 20390 | 164 | 20 | 12.1951 | |
| eyeh-varpipe | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.9665 | 98.0847 | 81.3995 | 77.6081 | 973 | 19 | 919 | 210 | 7 | 3.3333 | |
| ltrigg-rtg1 | INDEL | D6_15 | map_l100_m2_e0 | hetalt | 92.9853 | 88.2353 | 98.2759 | 77.6062 | 60 | 8 | 57 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.0580 | 85.1852 | 81.0345 | 77.6062 | 115 | 20 | 94 | 22 | 21 | 95.4545 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.5562 | 99.3991 | 99.7137 | 77.6038 | 6617 | 40 | 6617 | 19 | 5 | 26.3158 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.6246 | 94.1088 | 97.1901 | 77.6009 | 623 | 39 | 588 | 17 | 5 | 29.4118 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 33.6634 | 37.7778 | 30.3571 | 77.6000 | 17 | 28 | 17 | 39 | 34 | 87.1795 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 53.1925 | 58.9431 | 48.4642 | 77.5994 | 145 | 101 | 142 | 151 | 149 | 98.6755 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.4040 | 96.4646 | 92.4295 | 77.5992 | 2101 | 77 | 1868 | 153 | 139 | 90.8497 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.3251 | 99.4893 | 99.1616 | 77.5985 | 6623 | 34 | 6623 | 56 | 11 | 19.6429 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | * | 72.1859 | 56.5571 | 99.7506 | 77.5984 | 11601 | 8911 | 11601 | 29 | 5 | 17.2414 | |
| ckim-isaac | INDEL | D1_5 | map_siren | * | 88.4097 | 80.1927 | 98.5028 | 77.5975 | 2830 | 699 | 2829 | 43 | 19 | 44.1860 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l100_m2_e1 | * | 98.0955 | 97.0088 | 99.2068 | 77.5974 | 1881 | 58 | 1876 | 15 | 2 | 13.3333 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 37.7984 | 31.9149 | 46.3415 | 77.5956 | 15 | 32 | 19 | 22 | 21 | 95.4545 | |
| gduggal-bwafb | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.6826 | 98.0211 | 91.5640 | 77.5938 | 1486 | 30 | 1487 | 137 | 13 | 9.4891 | |
| egarrison-hhga | SNP | * | map_l100_m1_e0 | hetalt | 95.0000 | 92.6829 | 97.4359 | 77.5862 | 38 | 3 | 38 | 1 | 1 | 100.0000 | |
| egarrison-hhga | SNP | tv | map_l100_m1_e0 | hetalt | 95.0000 | 92.6829 | 97.4359 | 77.5862 | 38 | 3 | 38 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 91.2409 | 95.9430 | 86.9781 | 77.5847 | 875 | 37 | 875 | 131 | 121 | 92.3664 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 93.4478 | 94.6950 | 92.2330 | 77.5820 | 2981 | 167 | 2945 | 248 | 101 | 40.7258 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1530 | 98.6794 | 99.6313 | 77.5757 | 1345 | 18 | 1351 | 5 | 3 | 60.0000 | |
| ghariani-varprowl | SNP | * | map_l150_m0_e0 | homalt | 98.0874 | 96.5762 | 99.6467 | 77.5747 | 3949 | 140 | 3949 | 14 | 6 | 42.8571 | |
| ckim-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | hetalt | 91.6667 | 84.6154 | 100.0000 | 77.5701 | 22 | 4 | 24 | 0 | 0 | ||
| ckim-dragen | INDEL | D16_PLUS | map_l100_m2_e0 | hetalt | 91.6667 | 84.6154 | 100.0000 | 77.5701 | 22 | 4 | 24 | 0 | 0 | ||
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m2_e0 | hetalt | 91.6667 | 84.6154 | 100.0000 | 77.5701 | 22 | 4 | 24 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D16_PLUS | map_l100_m2_e0 | hetalt | 91.6667 | 84.6154 | 100.0000 | 77.5701 | 22 | 4 | 24 | 0 | 0 | ||
| anovak-vg | SNP | * | map_l150_m0_e0 | homalt | 84.1702 | 73.1719 | 99.0595 | 77.5693 | 2992 | 1097 | 2949 | 28 | 25 | 89.2857 | |
| qzeng-custom | INDEL | D6_15 | map_l100_m2_e1 | homalt | 80.0247 | 88.0597 | 73.3333 | 77.5641 | 59 | 8 | 77 | 28 | 3 | 10.7143 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.4086 | 85.9259 | 81.0345 | 77.5629 | 116 | 19 | 94 | 22 | 21 | 95.4545 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.4631 | 98.9319 | 100.0000 | 77.5605 | 1482 | 16 | 1503 | 0 | 0 | ||
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.1117 | 98.9729 | 99.2509 | 77.5593 | 1349 | 14 | 1325 | 10 | 5 | 50.0000 | |
| jli-custom | INDEL | I6_15 | map_siren | hetalt | 97.1429 | 94.4444 | 100.0000 | 77.5578 | 68 | 4 | 68 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.7238 | 95.4086 | 92.0974 | 77.5572 | 2078 | 100 | 1853 | 159 | 148 | 93.0818 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0176 | 98.6372 | 99.4008 | 77.5553 | 1520 | 21 | 1493 | 9 | 3 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5960 | 99.4864 | 99.7059 | 77.5541 | 1356 | 7 | 1356 | 4 | 2 | 50.0000 | |
| ghariani-varprowl | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0759 | 98.6453 | 88.1018 | 77.5526 | 3204 | 44 | 3221 | 435 | 34 | 7.8161 | |
| qzeng-custom | INDEL | I6_15 | map_siren | * | 71.0638 | 81.6393 | 62.9139 | 77.5520 | 249 | 56 | 285 | 168 | 8 | 4.7619 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.0066 | 99.5228 | 94.6144 | 77.5514 | 16894 | 81 | 16918 | 963 | 436 | 45.2752 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.0066 | 99.5228 | 94.6144 | 77.5514 | 16894 | 81 | 16918 | 963 | 436 | 45.2752 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.5017 | 79.3750 | 100.0000 | 77.5510 | 127 | 33 | 121 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I16_PLUS | func_cds | * | 95.6522 | 91.6667 | 100.0000 | 77.5510 | 11 | 1 | 11 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8506 | 100.0000 | 97.7273 | 77.5510 | 43 | 0 | 43 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m1_e0 | homalt | 59.4595 | 42.3077 | 100.0000 | 77.5510 | 11 | 15 | 11 | 0 | 0 | ||